1 LIN comparison of CASAL and Casal2 model configurations

This document compares the results of at least 2 CASAL model configurations (base and at least one sensitivity) and up to 6 Casal2 model configurations (3 BetaDiff and 3 ADOL-C).

The CASAL model sensitivity 1 has a smaller minimisation tolerance value than the CASAL base model (1e-6 vs. 2e-3).

The Casal2 ADOL-C and BetaDiff low tolerance models have a smaller tolerance value than the CASAL base model (1e-6 vs. 2e-3).

1.1 LIN model characteristics

The main characteristics of the Test Case LIN (ling) CASAL model are:

  • one stock, ages 3 - 25
  • one area
  • years 1972 - 2018, projection years 2019 - 2023
  • two time steps: Dec_Aug and Sep_Nov
  • two stock categories: male and female
  • natural mortality-at-age is double exponential
  • sex-specific maturity ogives specified by age
  • sex-specific von Bertalanffy age-length relationship
  • sex-specific length-weight relationship (\(W = aL^b\))
  • Beverton-Holt stock-recruitment relationship, with steepness (h) 0.84
  • ageing error
  • two surveys with sex-specific logistic selectivity
  • three fisheries, one with double normal selectivity and two with logistic selectivity

Observation data include:

  • survey indices
  • survey proportions-at-age
  • fishery proportions-at-age

Parameters estimated include:

  • B0
  • parameters for the natural mortality-at-age ogive
  • catchability (q) for the two surveys
  • parameters for the sex-specific selectivity curves for the two surveys
  • parameters for the sex-specific selectivity curves for the three fisheries
  • YCS (recruitment deviations)

1.2 R environment

## [1] "Tue Nov 16 15:19:56 2021"
## R version 4.1.2 (2021-11-01)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Debian GNU/Linux bookworm/sid
## 
## Matrix products: default
## BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.18.so
## 
## locale:
##  [1] LC_CTYPE=en_NZ.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_NZ.UTF-8        LC_COLLATE=en_NZ.UTF-8    
##  [5] LC_MONETARY=en_NZ.UTF-8    LC_MESSAGES=en_NZ.UTF-8   
##  [7] LC_PAPER=en_NZ.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=en_NZ.UTF-8 LC_IDENTIFICATION=C       
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
##  [1] Casal2_21.10   casal_2.30     devtools_2.4.2 usethis_2.1.3  rlist_0.4.6.2 
##  [6] ggthemes_4.2.4 gridExtra_2.3  coda_0.19-4    ggmcmc_1.5.1.1 ggplot2_3.3.5 
## [11] tidyr_1.1.4    huxtable_5.4.0 dplyr_1.0.7    plyr_1.8.6    
## 
## loaded via a namespace (and not attached):
##  [1] Rcpp_1.0.7         lattice_0.20-45    prettyunits_1.1.1  ps_1.6.0          
##  [5] assertthat_0.2.1   rprojroot_2.0.2    digest_0.6.28      utf8_1.2.2        
##  [9] R6_2.5.1           evaluate_0.14      pillar_1.6.4       rlang_0.4.12      
## [13] data.table_1.14.2  callr_3.7.0        jquerylib_0.1.4    rmarkdown_2.11    
## [17] desc_1.4.0         stringr_1.4.0      munsell_0.5.0      compiler_4.1.2    
## [21] xfun_0.28          pkgconfig_2.0.3    pkgbuild_1.2.0     htmltools_0.5.2   
## [25] tidyselect_1.1.1   tibble_3.1.6       reshape_0.8.8      fansi_0.5.0       
## [29] crayon_1.4.2       withr_2.4.2        grid_4.1.2         jsonlite_1.7.2    
## [33] GGally_2.1.2       gtable_0.3.0       lifecycle_1.0.1    DBI_1.1.1         
## [37] magrittr_2.0.1     scales_1.1.1       cli_3.1.0          stringi_1.7.5     
## [41] cachem_1.0.6       fs_1.5.0           remotes_2.4.1      testthat_3.1.0    
## [45] bslib_0.3.1        ellipsis_0.3.2     generics_0.1.1     vctrs_0.3.8       
## [49] RColorBrewer_1.1-2 tools_4.1.2        glue_1.5.0         purrr_0.3.4       
## [53] processx_3.5.2     pkgload_1.2.3      fastmap_1.1.0      yaml_2.2.1        
## [57] colorspace_2.0-2   sessioninfo_1.2.1  memoise_2.0.0      knitr_1.36        
## [61] sass_0.4.0

1.3 CASAL and Casal2 model output

source('../../R-functions/report_read_in_CASAL_MPD_files.R')
source('../../R-functions/report_read_in_Casal2_MPD_files.R')

1.4 Tables

Tables of parameter estimates and objective function components for the CASAL and Casal2 model MPD results

CASAL parameter estimates
rownamesBase_ModelSensitivity_1Percent_Diff
q[tan_sum].q         0.091280.091050.252
q[tan_aut].q         0.126200.125900.238
initialization.B0        309000.00000310700.00000-0.550
natural_mortality.ogive_all112.4900012.98000-3.923
natural_mortality.ogive_all20.132700.127803.693
natural_mortality.ogive_all30.381900.44990-17.806
natural_mortality.ogive_all40.350600.35390-0.941
selectivity[surveysum_sel].male1     4.738004.88100-3.018
selectivity[surveysum_sel].male2     1.750001.77200-1.257
selectivity[surveysum_sel].male3     0.610000.601601.377
selectivity[surveysum_sel].female1   5.460005.61300-2.802
selectivity[surveysum_sel].female2   2.206002.21500-0.408
selectivity[surveyaut_sel].male1     5.504005.64400-2.544
selectivity[surveyaut_sel].male2     2.314002.298000.691
selectivity[surveyaut_sel].male3     0.939200.933100.649
selectivity[surveyaut_sel].female1   5.920006.06200-2.399
selectivity[surveyaut_sel].female2   2.778002.738001.440
selectivity[trawl_sel].male1     8.370008.40400-0.406
selectivity[trawl_sel].male2     1.972001.947001.268
selectivity[trawl_sel].male3     61.65000200.00000-224.412
selectivity[trawl_sel].male4     1.041001.021001.921
selectivity[trawl_sel].female1   8.664008.74100-0.889
selectivity[trawl_sel].female2   2.100002.088000.571
selectivity[trawl_sel].female3   43.3100040.380006.765
selectivity[line_home_sel].male1     11.450008.5830025.039
selectivity[line_home_sel].male2     8.590004.5470047.066
selectivity[line_home_sel].male3     0.380100.2691029.203
selectivity[line_home_sel].female1   9.616009.531000.884
selectivity[line_home_sel].female2   3.875003.685004.903
selectivity[line_spawn_sel].male1     18.3000014.0400023.279
selectivity[line_spawn_sel].male2     13.6700010.0100026.774
selectivity[line_spawn_sel].male3     1.868001.1730037.206
selectivity[line_spawn_sel].female1   9.746009.713000.339
selectivity[line_spawn_sel].female2   3.008002.894003.790
recruitment.YCS1      1.000001.000000.000
recruitment.YCS2      1.000001.000000.000
recruitment.YCS3      1.000001.000000.000
recruitment.YCS4      1.000001.000000.000
recruitment.YCS5      0.485000.466203.876
recruitment.YCS6      0.458300.450101.789
recruitment.YCS7      0.568600.564700.686
recruitment.YCS8      0.566700.566700.000
recruitment.YCS9      0.486100.49070-0.946
recruitment.YCS10     0.555000.56720-2.198
recruitment.YCS11     0.563200.57880-2.770
recruitment.YCS12     0.687600.71090-3.389
recruitment.YCS13     0.620300.63610-2.547
recruitment.YCS14     0.790600.80840-2.251
recruitment.YCS15     0.464300.46930-1.077
recruitment.YCS16     0.700800.70730-0.928
recruitment.YCS17     0.410100.41050-0.098
recruitment.YCS18     0.515000.514500.097
recruitment.YCS19     0.341600.34220-0.176
recruitment.YCS20     0.348300.347300.287
recruitment.YCS21     0.436100.43820-0.482
recruitment.YCS22     0.480600.475001.165
recruitment.YCS23     0.452200.451300.199
recruitment.YCS24     0.491700.49480-0.630
recruitment.YCS25     0.469100.47070-0.341
recruitment.YCS26     0.799300.80490-0.701
recruitment.YCS27     0.790100.79210-0.253
recruitment.YCS28     0.826100.83110-0.605
recruitment.YCS29     0.707600.71250-0.692
recruitment.YCS30     0.551700.55430-0.471
recruitment.YCS31     0.475200.47680-0.337
recruitment.YCS32     0.461700.461400.065
recruitment.YCS33     0.555000.554300.126
recruitment.YCS34     0.546700.542100.841
recruitment.YCS35     0.483200.482500.145
recruitment.YCS36     0.550200.549900.055
recruitment.YCS37     0.615300.61580-0.081
recruitment.YCS38     0.775700.774700.129
recruitment.YCS39     0.631100.630600.079
recruitment.YCS40     0.775500.773500.258
recruitment.YCS41     0.642900.639300.560
recruitment.YCS42     0.706700.699401.033
recruitment.YCS43     0.654300.648600.871
recruitment.YCS44     0.510000.506200.745
recruitment.YCS45     0.586200.58730-0.188
recruitment.YCS46     0.603500.589302.353
recruitment.YCS47     0.576800.574500.399
Casal2 parameter estimates
rownamesbetadiff_casal_flags_onbetadiff_casal_flags_offbetadiff_casal_flags_on_low_toladolc_casal_flags_onadolc_casal_flags_offadolc_casal_flags_on_low_tol
process[Recruitment].b0              308529.00000308529.00000310577.00000308529.00000308529.00000310577.00000
catchability[summerTANq].q               0.091370.091370.091060.091370.091370.09106
catchability[autumnTANq].q               0.126070.126070.125940.126070.126070.12594
selectivity[M_all].x0              12.4965012.4965012.9844012.4965012.4965012.98440
selectivity[M_all].y0              0.132620.132620.127970.132620.132620.12797
selectivity[M_all].y1              0.382800.382800.447260.382800.382800.44726
selectivity[M_all].y2              0.351130.351130.353730.351130.351130.35373
selectivity[summerTANSel_m].a50             4.739884.739884.876454.739884.739884.87645
selectivity[summerTANSel_m].ato95           1.744591.744591.770291.744591.744591.77029
selectivity[summerTANSel_m].alpha           0.609950.609950.601840.609950.609950.60184
selectivity[summerTANSel_f].a50             5.461115.461115.608075.461115.461115.60807
selectivity[summerTANSel_f].ato95           2.203402.203402.214202.203402.203402.21420
selectivity[autumnTANSel_m].a50             5.509825.509825.639725.509825.509825.63972
selectivity[autumnTANSel_m].ato95           2.312712.312712.297812.312712.312712.29781
selectivity[autumnTANSel_m].alpha           0.941730.941730.933200.941730.941730.93320
selectivity[autumnTANSel_f].a50             5.915745.915746.058485.915745.915746.05848
selectivity[autumnTANSel_f].ato95           2.770202.770202.738462.770202.770202.73846
selectivity[trwlFSel_m].mu              8.369198.369198.402398.369198.369198.40239
selectivity[trwlFSel_m].sigma_l         1.970231.970231.947351.970231.970231.94735
selectivity[trwlFSel_m].sigma_r         61.5229061.52290200.0000061.5229061.52290200.00000
selectivity[trwlFSel_m].alpha           1.042761.042761.020851.042761.042761.02085
selectivity[trwlFSel_f].mu              8.658548.658548.739498.658548.658548.73949
selectivity[trwlFSel_f].sigma_l         2.096562.096562.088492.096562.096562.08849
selectivity[trwlFSel_f].sigma_r         43.1639043.1639040.5947043.1639043.1639040.59470
selectivity[lineHomeFSel_m].a50             11.4560011.456008.6083511.4560011.456008.60835
selectivity[lineHomeFSel_m].ato95           8.599588.599584.591698.599588.599584.59169
selectivity[lineHomeFSel_m].alpha           0.380220.380220.269930.380220.380220.26993
selectivity[lineHomeFSel_f].a50             9.614769.614769.533529.614769.614769.53352
selectivity[lineHomeFSel_f].ato95           3.870143.870143.690643.870143.870143.69064
selectivity[lineSpawnFSel_m].a50             18.2151018.2151014.0467018.2151018.2151014.04670
selectivity[lineSpawnFSel_m].ato95           13.5995013.5995010.0261013.5995013.5995010.02610
selectivity[lineSpawnFSel_m].alpha           1.856341.856341.174491.856341.856341.17449
selectivity[lineSpawnFSel_f].a50             9.738629.738629.714789.738629.738629.71478
selectivity[lineSpawnFSel_f].ato95           2.993872.993872.896702.993872.993872.89670
process[Recruitment].ycs_values{1972}0.483790.483790.466420.483790.483790.46642
process[Recruitment].ycs_values{1973}0.461220.461220.450200.461220.461220.45020
process[Recruitment].ycs_values{1974}0.568370.568370.564540.568370.568370.56454
process[Recruitment].ycs_values{1975}0.566520.566520.566880.566520.566520.56688
process[Recruitment].ycs_values{1976}0.486350.486350.490810.486350.486350.49081
process[Recruitment].ycs_values{1977}0.554130.554130.567170.554130.554130.56717
process[Recruitment].ycs_values{1978}0.563160.563160.578550.563160.563160.57855
process[Recruitment].ycs_values{1979}0.688990.688990.710940.688990.688990.71094
process[Recruitment].ycs_values{1980}0.620930.620930.636190.620930.620930.63619
process[Recruitment].ycs_values{1981}0.792470.792470.808020.792470.792470.80802
process[Recruitment].ycs_values{1982}0.465070.465070.469290.465070.465070.46929
process[Recruitment].ycs_values{1983}0.699670.699670.707060.699670.699670.70706
process[Recruitment].ycs_values{1984}0.409950.409950.410420.409950.409950.41042
process[Recruitment].ycs_values{1985}0.515400.515400.514560.515400.515400.51456
process[Recruitment].ycs_values{1986}0.341310.341310.342120.341310.341310.34212
process[Recruitment].ycs_values{1987}0.347600.347600.347280.347600.347600.34728
process[Recruitment].ycs_values{1988}0.437910.437910.438260.437910.437910.43826
process[Recruitment].ycs_values{1989}0.479240.479240.475010.479240.479240.47501
process[Recruitment].ycs_values{1990}0.451810.451810.451330.451810.451810.45133
process[Recruitment].ycs_values{1991}0.492640.492640.494790.492640.492640.49479
process[Recruitment].ycs_values{1992}0.469180.469180.470700.469180.469180.47070
process[Recruitment].ycs_values{1993}0.797910.797910.804860.797910.797910.80486
process[Recruitment].ycs_values{1994}0.791280.791280.792080.791280.791280.79208
process[Recruitment].ycs_values{1995}0.825380.825380.831090.825380.825380.83109
process[Recruitment].ycs_values{1996}0.707280.707280.712490.707280.707280.71249
process[Recruitment].ycs_values{1997}0.552060.552060.554270.552060.552060.55427
process[Recruitment].ycs_values{1998}0.475080.475080.476830.475080.475080.47683
process[Recruitment].ycs_values{1999}0.461190.461190.461400.461190.461190.46140
process[Recruitment].ycs_values{2000}0.555750.555750.554420.555750.555750.55442
process[Recruitment].ycs_values{2001}0.545460.545460.542060.545460.545460.54206
process[Recruitment].ycs_values{2002}0.483730.483730.482630.483730.483730.48263
process[Recruitment].ycs_values{2003}0.549890.549890.549930.549890.549890.54993
process[Recruitment].ycs_values{2004}0.614180.614180.615780.614180.614180.61578
process[Recruitment].ycs_values{2005}0.777120.777120.774620.777120.777120.77462
process[Recruitment].ycs_values{2006}0.631300.631300.630520.631300.631300.63052
process[Recruitment].ycs_values{2007}0.773770.773770.773450.773770.773770.77345
process[Recruitment].ycs_values{2008}0.642510.642510.639280.642510.642510.63928
process[Recruitment].ycs_values{2009}0.706490.706490.699350.706490.706490.69935
process[Recruitment].ycs_values{2010}0.653120.653120.648710.653120.653120.64871
process[Recruitment].ycs_values{2011}0.511360.511360.506230.511360.511360.50623
process[Recruitment].ycs_values{2012}0.585560.585560.587380.585560.585560.58738
process[Recruitment].ycs_values{2013}0.600640.600640.589120.600640.600640.58912
process[Recruitment].ycs_values{2014}0.576010.576010.574500.576010.576010.57450
Casal2 parameter estimates: Percent Difference from betadiff_casal_flags_on
rownamesbetadiff_casal_flags_onbetadiff_casal_flags_offbetadiff_casal_flags_on_low_toladolc_casal_flags_onadolc_casal_flags_offadolc_casal_flags_on_low_tol
process[Recruitment].b0              0.0000.000-0.6640.0000.000-0.664
catchability[summerTANq].q               0.0000.0000.3440.0000.0000.344
catchability[autumnTANq].q               0.0000.0000.1050.0000.0000.105
selectivity[M_all].x0              0.0000.000-3.9040.0000.000-3.904
selectivity[M_all].y0              0.0000.0003.5100.0000.0003.510
selectivity[M_all].y1              0.0000.000-16.8400.0000.000-16.840
selectivity[M_all].y2              0.0000.000-0.7410.0000.000-0.741
selectivity[summerTANSel_m].a50             0.0000.000-2.8810.0000.000-2.881
selectivity[summerTANSel_m].ato95           0.0000.000-1.4730.0000.000-1.473
selectivity[summerTANSel_m].alpha           0.0000.0001.3290.0000.0001.329
selectivity[summerTANSel_f].a50             0.0000.000-2.6910.0000.000-2.691
selectivity[summerTANSel_f].ato95           0.0000.000-0.4900.0000.000-0.490
selectivity[autumnTANSel_m].a50             0.0000.000-2.3580.0000.000-2.358
selectivity[autumnTANSel_m].ato95           0.0000.0000.6440.0000.0000.644
selectivity[autumnTANSel_m].alpha           0.0000.0000.9060.0000.0000.906
selectivity[autumnTANSel_f].a50             0.0000.000-2.4130.0000.000-2.413
selectivity[autumnTANSel_f].ato95           0.0000.0001.1460.0000.0001.146
selectivity[trwlFSel_m].mu              0.0000.000-0.3970.0000.000-0.397
selectivity[trwlFSel_m].sigma_l         0.0000.0001.1610.0000.0001.161
selectivity[trwlFSel_m].sigma_r         0.0000.000-225.0820.0000.000-225.082
selectivity[trwlFSel_m].alpha           0.0000.0002.1010.0000.0002.101
selectivity[trwlFSel_f].mu              0.0000.000-0.9350.0000.000-0.935
selectivity[trwlFSel_f].sigma_l         0.0000.0000.3850.0000.0000.385
selectivity[trwlFSel_f].sigma_r         0.0000.0005.9520.0000.0005.952
selectivity[lineHomeFSel_m].a50             0.0000.00024.8570.0000.00024.857
selectivity[lineHomeFSel_m].ato95           0.0000.00046.6060.0000.00046.606
selectivity[lineHomeFSel_m].alpha           0.0000.00029.0070.0000.00029.007
selectivity[lineHomeFSel_f].a50             0.0000.0000.8450.0000.0000.845
selectivity[lineHomeFSel_f].ato95           0.0000.0004.6380.0000.0004.638
selectivity[lineSpawnFSel_m].a50             0.0000.00022.8840.0000.00022.884
selectivity[lineSpawnFSel_m].ato95           0.0000.00026.2760.0000.00026.276
selectivity[lineSpawnFSel_m].alpha           0.0000.00036.7310.0000.00036.731
selectivity[lineSpawnFSel_f].a50             0.0000.0000.2450.0000.0000.245
selectivity[lineSpawnFSel_f].ato95           0.0000.0003.2460.0000.0003.246
process[Recruitment].ycs_values{1972}0.0000.0003.5890.0000.0003.589
process[Recruitment].ycs_values{1973}0.0000.0002.3890.0000.0002.389
process[Recruitment].ycs_values{1974}0.0000.0000.6750.0000.0000.675
process[Recruitment].ycs_values{1975}0.0000.000-0.0640.0000.000-0.064
process[Recruitment].ycs_values{1976}0.0000.000-0.9160.0000.000-0.916
process[Recruitment].ycs_values{1977}0.0000.000-2.3530.0000.000-2.353
process[Recruitment].ycs_values{1978}0.0000.000-2.7330.0000.000-2.733
process[Recruitment].ycs_values{1979}0.0000.000-3.1850.0000.000-3.185
process[Recruitment].ycs_values{1980}0.0000.000-2.4570.0000.000-2.457
process[Recruitment].ycs_values{1981}0.0000.000-1.9620.0000.000-1.962
process[Recruitment].ycs_values{1982}0.0000.000-0.9060.0000.000-0.906
process[Recruitment].ycs_values{1983}0.0000.000-1.0560.0000.000-1.056
process[Recruitment].ycs_values{1984}0.0000.000-0.1150.0000.000-0.115
process[Recruitment].ycs_values{1985}0.0000.0000.1620.0000.0000.162
process[Recruitment].ycs_values{1986}0.0000.000-0.2360.0000.000-0.236
process[Recruitment].ycs_values{1987}0.0000.0000.0910.0000.0000.091
process[Recruitment].ycs_values{1988}0.0000.000-0.0790.0000.000-0.079
process[Recruitment].ycs_values{1989}0.0000.0000.8840.0000.0000.884
process[Recruitment].ycs_values{1990}0.0000.0000.1060.0000.0000.106
process[Recruitment].ycs_values{1991}0.0000.000-0.4360.0000.000-0.436
process[Recruitment].ycs_values{1992}0.0000.000-0.3250.0000.000-0.325
process[Recruitment].ycs_values{1993}0.0000.000-0.8710.0000.000-0.871
process[Recruitment].ycs_values{1994}0.0000.000-0.1020.0000.000-0.102
process[Recruitment].ycs_values{1995}0.0000.000-0.6910.0000.000-0.691
process[Recruitment].ycs_values{1996}0.0000.000-0.7360.0000.000-0.736
process[Recruitment].ycs_values{1997}0.0000.000-0.4000.0000.000-0.400
process[Recruitment].ycs_values{1998}0.0000.000-0.3680.0000.000-0.368
process[Recruitment].ycs_values{1999}0.0000.000-0.0450.0000.000-0.045
process[Recruitment].ycs_values{2000}0.0000.0000.2390.0000.0000.239
process[Recruitment].ycs_values{2001}0.0000.0000.6230.0000.0000.623
process[Recruitment].ycs_values{2002}0.0000.0000.2270.0000.0000.227
process[Recruitment].ycs_values{2003}0.0000.000-0.0080.0000.000-0.008
process[Recruitment].ycs_values{2004}0.0000.000-0.2600.0000.000-0.260
process[Recruitment].ycs_values{2005}0.0000.0000.3210.0000.0000.321
process[Recruitment].ycs_values{2006}0.0000.0000.1230.0000.0000.123
process[Recruitment].ycs_values{2007}0.0000.0000.0420.0000.0000.042
process[Recruitment].ycs_values{2008}0.0000.0000.5030.0000.0000.503
process[Recruitment].ycs_values{2009}0.0000.0001.0100.0000.0001.010
process[Recruitment].ycs_values{2010}0.0000.0000.6740.0000.0000.674
process[Recruitment].ycs_values{2011}0.0000.0001.0040.0000.0001.004
process[Recruitment].ycs_values{2012}0.0000.000-0.3110.0000.000-0.311
process[Recruitment].ycs_values{2013}0.0000.0001.9180.0000.0001.918
process[Recruitment].ycs_values{2014}0.0000.0000.2620.0000.0000.262

CASAL objective function component values
ComponentBase_ModelSensitivity_1
Tangaroa_bio_autumn-6.829-6.834
Tangaroa_bio_summer-23.880-23.960
Tangaroa_propn_at_age_aut175.700175.800
Tangaroa_propn_at_age_summer835.900835.600
longline_Campbell_home_propn_at_age275.700275.400
longline_Puysegur_spawn_propn_at_age363.300363.300
trawl_observer_propn_at_age682.600682.300
prior_on_q[tan_sum].q-2.364-2.366
prior_on_q[tan_aut].q-2.033-2.037
prior_on_initialization.B012.64012.650
prior_on_natural_mortality.ogive_all0.0000.000
prior_on_selectivity[surveysum_sel].male0.0000.000
prior_on_selectivity[surveysum_sel].female0.0000.000
prior_on_selectivity[surveyaut_sel].male0.0000.000
prior_on_selectivity[surveyaut_sel].female0.0000.000
prior_on_selectivity[trawl_sel].male0.0000.000
prior_on_selectivity[trawl_sel].female0.0000.000
prior_on_selectivity[line_home_sel].male0.0000.000
prior_on_selectivity[line_home_sel].female0.0000.000
prior_on_selectivity[line_spawn_sel].male0.0000.000
prior_on_selectivity[line_spawn_sel].female0.0000.000
prior_on_recruitment.YCS-14.440-14.370
clp10.0000.000
clp20.0000.000
clp30.0000.000
YCS_average_10.9080.903
Total2297.0002296.000
Casal2 objective function component values
rownamesbetadiff_casal_flags_onbetadiff_casal_flags_offbetadiff_casal_flags_on_low_toladolc_casal_flags_onadolc_casal_flags_offadolc_casal_flags_on_low_tol
observation->summerTANbiomass-1992                 -1.693-1.693-1.679-1.693-1.693-1.679
observation->summerTANbiomass-1993                 -1.353-1.353-1.331-1.353-1.353-1.331
observation->summerTANbiomass-1994                 -0.975-0.975-0.991-0.975-0.975-0.991
observation->summerTANbiomass-2001                 0.4300.4300.3540.4300.4300.354
observation->summerTANbiomass-2002                 -1.778-1.778-1.786-1.778-1.778-1.786
observation->summerTANbiomass-2003                 -1.685-1.685-1.693-1.685-1.685-1.693
observation->summerTANbiomass-2004                 -1.598-1.598-1.586-1.598-1.598-1.586
observation->summerTANbiomass-2005                 -1.657-1.657-1.656-1.657-1.657-1.656
observation->summerTANbiomass-2006                 -1.143-1.143-1.153-1.143-1.143-1.153
observation->summerTANbiomass-2007                 -1.162-1.162-1.180-1.162-1.162-1.180
observation->summerTANbiomass-2008                 -1.568-1.568-1.553-1.568-1.568-1.553
observation->summerTANbiomass-2009                 -1.700-1.700-1.705-1.700-1.700-1.705
observation->summerTANbiomass-2010                 -1.672-1.672-1.678-1.672-1.672-1.678
observation->summerTANbiomass-2012                 -1.554-1.554-1.558-1.554-1.554-1.558
observation->summerTANbiomass-2013                 -1.669-1.669-1.667-1.669-1.669-1.667
observation->summerTANbiomass-2015                 -1.582-1.582-1.570-1.582-1.582-1.570
observation->summerTANbiomass-2017                 -1.526-1.526-1.528-1.526-1.526-1.528
observation->Tangaroa_propn_at_age_summer-1990                 44.21844.21844.39344.21844.21844.393
observation->Tangaroa_propn_at_age_summer-1992                 51.99351.99351.75351.99351.99351.753
observation->Tangaroa_propn_at_age_summer-1993                 50.20050.20050.16850.20050.20050.168
observation->Tangaroa_propn_at_age_summer-1994                 49.74349.74349.78549.74349.74349.785
observation->Tangaroa_propn_at_age_summer-2001                 48.35548.35548.23748.35548.35548.237
observation->Tangaroa_propn_at_age_summer-2002                 47.83047.83047.87947.83047.83047.879
observation->Tangaroa_propn_at_age_summer-2003                 48.44248.44248.62048.44248.44248.620
observation->Tangaroa_propn_at_age_summer-2004                 44.82344.82344.86544.82344.82344.865
observation->Tangaroa_propn_at_age_summer-2005                 43.09743.09743.11743.09743.09743.117
observation->Tangaroa_propn_at_age_summer-2006                 43.89143.89144.05843.89143.89144.058
observation->Tangaroa_propn_at_age_summer-2007                 41.84841.84841.84141.84841.84841.841
observation->Tangaroa_propn_at_age_summer-2008                 45.22545.22545.26645.22545.22545.266
observation->Tangaroa_propn_at_age_summer-2009                 46.84446.84446.80646.84446.84446.806
observation->Tangaroa_propn_at_age_summer-2010                 47.12847.12847.20247.12847.12847.202
observation->Tangaroa_propn_at_age_summer-2012                 44.35344.35344.18344.35344.35344.183
observation->Tangaroa_propn_at_age_summer-2013                 47.25147.25147.02147.25147.25147.021
observation->Tangaroa_propn_at_age_summer-2015                 46.47346.47346.34246.47346.47346.342
observation->Tangaroa_propn_at_age_summer-2017                 44.18244.18244.08244.18244.18244.082
observation->autumnTANbiomass-1992                 -1.558-1.558-1.572-1.558-1.558-1.572
observation->autumnTANbiomass-1993                 -1.741-1.741-1.733-1.741-1.741-1.733
observation->autumnTANbiomass-1996                 -1.779-1.779-1.779-1.779-1.779-1.779
observation->autumnTANbiomass-1998                 -1.750-1.750-1.750-1.750-1.750-1.750
observation->Tangaroa_propn_at_age_autumn-1992                 44.58944.58944.44344.58944.58944.443
observation->Tangaroa_propn_at_age_autumn-1993                 45.48445.48445.44345.48445.48445.443
observation->Tangaroa_propn_at_age_autumn-1996                 42.18442.18442.29542.18442.18442.295
observation->Tangaroa_propn_at_age_autumn-1998                 43.46443.46443.61043.46443.46443.610
observation->trawl_propn_at_age-1992                 36.06736.06735.94436.06736.06735.944
observation->trawl_propn_at_age-1993                 27.51627.51627.47627.51627.51627.476
observation->trawl_propn_at_age-1994                 25.81925.81925.76425.81925.81925.764
observation->trawl_propn_at_age-1996                 28.39428.39428.39728.39428.39428.397
observation->trawl_propn_at_age-1998                 24.91524.91524.91024.91524.91524.910
observation->trawl_propn_at_age-2001                 24.58024.58024.54224.58024.58024.542
observation->trawl_propn_at_age-2002                 26.77026.77026.79226.77026.77026.792
observation->trawl_propn_at_age-2003                 34.56434.56434.51134.56434.56434.511
observation->trawl_propn_at_age-2004                 29.60829.60829.60829.60829.60829.608
observation->trawl_propn_at_age-2005                 30.14730.14730.16630.14730.14730.166
observation->trawl_propn_at_age-2006                 33.62933.62933.71433.62933.62933.714
observation->trawl_propn_at_age-2007                 26.63526.63526.58826.63526.63526.588
observation->trawl_propn_at_age-2008                 27.05927.05927.07627.05927.05927.076
observation->trawl_propn_at_age-2009                 37.21337.21337.23737.21337.21337.237
observation->trawl_propn_at_age-2010                 30.64830.64830.69430.64830.64830.694
observation->trawl_propn_at_age-2011                 31.26631.26631.26031.26631.26631.260
observation->trawl_propn_at_age-2012                 32.32532.32532.36632.32532.32532.366
observation->trawl_propn_at_age-2013                 37.07237.07236.94337.07237.07236.943
observation->trawl_propn_at_age-2014                 30.64030.64030.64230.64030.64030.642
observation->trawl_propn_at_age-2015                 33.45633.45633.47433.45633.45633.474
observation->trawl_propn_at_age-2016                 36.53236.53236.48236.53236.53236.482
observation->trawl_propn_at_age-2017                 37.75537.75537.70837.75537.75537.708
observation->longline_Campbell_home_propn_at_age-1999                 45.34845.34845.25645.34845.34845.256
observation->longline_Campbell_home_propn_at_age-2001                 31.96531.96531.95031.96531.96531.950
observation->longline_Campbell_home_propn_at_age-2003                 28.64428.64428.67528.64428.64428.675
observation->longline_Campbell_home_propn_at_age-2005                 32.75032.75032.77632.75032.75032.776
observation->longline_Campbell_home_propn_at_age-2009                 26.03326.03325.61126.03326.03325.611
observation->longline_Campbell_home_propn_at_age-2010                 24.30224.30224.46124.30224.30224.461
observation->longline_Campbell_home_propn_at_age-2011                 28.87828.87828.93528.87828.87828.935
observation->longline_Campbell_home_propn_at_age-2012                 32.25832.25832.38832.25832.25832.388
observation->longline_Campbell_home_propn_at_age-2014                 25.49525.49525.35725.49525.49525.357
observation->longline_Puyseger_home_propn_at_age-2000                 42.74542.74542.68042.74542.74542.680
observation->longline_Puyseger_home_propn_at_age-2001                 31.77031.77031.90031.77031.77031.900
observation->longline_Puyseger_home_propn_at_age-2002                 39.97839.97839.99839.97839.97839.998
observation->longline_Puyseger_home_propn_at_age-2003                 43.52743.52743.51143.52743.52743.511
observation->longline_Puyseger_home_propn_at_age-2004                 39.95739.95740.01539.95739.95740.015
observation->longline_Puyseger_home_propn_at_age-2005                 25.53225.53225.35825.53225.53225.358
observation->longline_Puyseger_home_propn_at_age-2006                 35.21035.21035.42635.21035.21035.426
observation->longline_Puyseger_home_propn_at_age-2007                 33.98133.98133.78233.98133.98133.782
observation->longline_Puyseger_home_propn_at_age-2008                 19.13919.13919.11319.13919.13919.113
observation->longline_Puyseger_home_propn_at_age-2010                 24.23824.23824.36624.23824.23824.366
observation->longline_Puyseger_home_propn_at_age-2017                 27.20027.20027.09327.20027.20027.093
prior->B0->process[Recruitment].b0              12.64012.64012.64612.64012.64012.646
prior->summerTANq->catchability[summerTANq].q               -2.363-2.363-2.365-2.363-2.363-2.365
prior->autumnTANq->catchability[autumnTANq].q               -2.035-2.035-2.037-2.035-2.035-2.037
prior->M_all_x0->selectivity[M_all].x0              0.0000.0000.0000.0000.0000.000
prior->M_all_y0->selectivity[M_all].y0              0.0000.0000.0000.0000.0000.000
prior->M_all_y1->selectivity[M_all].y1              0.0000.0000.0000.0000.0000.000
prior->M_all_y2->selectivity[M_all].y2              0.0000.0000.0000.0000.0000.000
prior->selectivity[summerTANSel_m].a50             0.0000.0000.0000.0000.0000.000
prior->selectivity[summerTANSel_m].ato95           0.0000.0000.0000.0000.0000.000
prior->selectivity[summerTANSel_m].alpha           0.0000.0000.0000.0000.0000.000
prior->selectivity[summerTANSel_f].a50             0.0000.0000.0000.0000.0000.000
prior->selectivity[summerTANSel_f].ato95           0.0000.0000.0000.0000.0000.000
prior->selectivity[autumnTANSel_m].a50             0.0000.0000.0000.0000.0000.000
prior->selectivity[autumnTANSel_m].ato95           0.0000.0000.0000.0000.0000.000
prior->selectivity[autumnTANSel_m].alpha           0.0000.0000.0000.0000.0000.000
prior->selectivity[autumnTANSel_f].a50             0.0000.0000.0000.0000.0000.000
prior->selectivity[autumnTANSel_f].ato95           0.0000.0000.0000.0000.0000.000
prior->selectivity[trwlFSel_m].mu              0.0000.0000.0000.0000.0000.000
prior->selectivity[trwlFSel_m].sigma_l         0.0000.0000.0000.0000.0000.000
prior->selectivity[trwlFSel_m].sigma_r         0.0000.0000.0000.0000.0000.000
prior->selectivity[trwlFSel_m].alpha           0.0000.0000.0000.0000.0000.000
prior->selectivity[trwlFSel_f].mu              0.0000.0000.0000.0000.0000.000
prior->selectivity[trwlFSel_f].sigma_l         0.0000.0000.0000.0000.0000.000
prior->selectivity[trwlFSel_f].sigma_r         0.0000.0000.0000.0000.0000.000
prior->selectivity[lineHomeFSel_m].a50             0.0000.0000.0000.0000.0000.000
prior->selectivity[lineHomeFSel_m].ato95           0.0000.0000.0000.0000.0000.000
prior->selectivity[lineHomeFSel_m].alpha           0.0000.0000.0000.0000.0000.000
prior->selectivity[lineHomeFSel_f].a50             0.0000.0000.0000.0000.0000.000
prior->selectivity[lineHomeFSel_f].ato95           0.0000.0000.0000.0000.0000.000
prior->selectivity[lineSpawnFSel_m].a50             0.0000.0000.0000.0000.0000.000
prior->selectivity[lineSpawnFSel_m].ato95           0.0000.0000.0000.0000.0000.000
prior->selectivity[lineSpawnFSel_m].alpha           0.0000.0000.0000.0000.0000.000
prior->selectivity[lineSpawnFSel_f].a50             0.0000.0000.0000.0000.0000.000
prior->selectivity[lineSpawnFSel_f].ato95           0.0000.0000.0000.0000.0000.000
prior->process[Recruitment].ycs_values{1972}-0.378-0.378-0.365-0.378-0.378-0.365
prior->process[Recruitment].ycs_values{1973}-0.360-0.360-0.349-0.360-0.360-0.349
prior->process[Recruitment].ycs_values{1974}-0.397-0.397-0.398-0.397-0.397-0.398
prior->process[Recruitment].ycs_values{1975}-0.398-0.398-0.398-0.398-0.398-0.398
prior->process[Recruitment].ycs_values{1976}-0.380-0.380-0.383-0.380-0.380-0.383
prior->process[Recruitment].ycs_values{1977}-0.399-0.399-0.398-0.399-0.399-0.398
prior->process[Recruitment].ycs_values{1978}-0.398-0.398-0.396-0.398-0.398-0.396
prior->process[Recruitment].ycs_values{1979}-0.335-0.335-0.316-0.335-0.335-0.316
prior->process[Recruitment].ycs_values{1980}-0.380-0.380-0.372-0.380-0.380-0.372
prior->process[Recruitment].ycs_values{1981}-0.231-0.231-0.213-0.231-0.231-0.213
prior->process[Recruitment].ycs_values{1982}-0.364-0.364-0.367-0.364-0.364-0.367
prior->process[Recruitment].ycs_values{1983}-0.326-0.326-0.319-0.326-0.326-0.319
prior->process[Recruitment].ycs_values{1984}-0.291-0.291-0.292-0.291-0.291-0.292
prior->process[Recruitment].ycs_values{1985}-0.394-0.394-0.393-0.394-0.394-0.393
prior->process[Recruitment].ycs_values{1986}-0.114-0.114-0.117-0.114-0.114-0.117
prior->process[Recruitment].ycs_values{1987}-0.135-0.135-0.134-0.135-0.135-0.134
prior->process[Recruitment].ycs_values{1988}-0.334-0.334-0.334-0.334-0.334-0.334
prior->process[Recruitment].ycs_values{1989}-0.375-0.375-0.372-0.375-0.375-0.372
prior->process[Recruitment].ycs_values{1990}-0.350-0.350-0.350-0.350-0.350-0.350
prior->process[Recruitment].ycs_values{1991}-0.384-0.384-0.385-0.384-0.384-0.385
prior->process[Recruitment].ycs_values{1992}-0.367-0.367-0.369-0.367-0.367-0.369
prior->process[Recruitment].ycs_values{1993}-0.225-0.225-0.217-0.225-0.225-0.217
prior->process[Recruitment].ycs_values{1994}-0.233-0.233-0.232-0.233-0.233-0.232
prior->process[Recruitment].ycs_values{1995}-0.192-0.192-0.185-0.192-0.192-0.185
prior->process[Recruitment].ycs_values{1996}-0.319-0.319-0.315-0.319-0.319-0.315
prior->process[Recruitment].ycs_values{1997}-0.399-0.399-0.399-0.399-0.399-0.399
prior->process[Recruitment].ycs_values{1998}-0.372-0.372-0.373-0.372-0.372-0.373
prior->process[Recruitment].ycs_values{1999}-0.360-0.360-0.360-0.360-0.360-0.360
prior->process[Recruitment].ycs_values{2000}-0.399-0.399-0.399-0.399-0.399-0.399
prior->process[Recruitment].ycs_values{2001}-0.399-0.399-0.399-0.399-0.399-0.399
prior->process[Recruitment].ycs_values{2002}-0.378-0.378-0.377-0.378-0.378-0.377
prior->process[Recruitment].ycs_values{2003}-0.399-0.399-0.399-0.399-0.399-0.399
prior->process[Recruitment].ycs_values{2004}-0.383-0.383-0.383-0.383-0.383-0.383
prior->process[Recruitment].ycs_values{2005}-0.249-0.249-0.251-0.249-0.249-0.251
prior->process[Recruitment].ycs_values{2006}-0.375-0.375-0.375-0.375-0.375-0.375
prior->process[Recruitment].ycs_values{2007}-0.252-0.252-0.253-0.252-0.252-0.253
prior->process[Recruitment].ycs_values{2008}-0.368-0.368-0.370-0.368-0.368-0.370
prior->process[Recruitment].ycs_values{2009}-0.320-0.320-0.326-0.320-0.320-0.326
prior->process[Recruitment].ycs_values{2010}-0.362-0.362-0.364-0.362-0.362-0.364
prior->process[Recruitment].ycs_values{2011}-0.392-0.392-0.390-0.392-0.392-0.390
prior->process[Recruitment].ycs_values{2012}-0.394-0.394-0.393-0.394-0.394-0.393
prior->process[Recruitment].ycs_values{2013}-0.389-0.389-0.393-0.389-0.389-0.393
prior->process[Recruitment].ycs_values{2014}-0.396-0.396-0.396-0.396-0.396-0.396
additional_prior->YCS_average_1                 0.9080.9080.9040.9080.9080.904
total_score                 2296.9702296.9702296.1402296.9702296.9702296.140

## [1] "CASAL base model convergence information"
## [1] "fmm: have converged: t = 0.00198541 f = 2297.19"                                                        
## [2] "Successful convergence in optimise"                                                                     
## [3] "Minimiser achieved convergence after 53 quasi-Newton iterations using 91 objective function evaluations"
## [1] ""
## [1] "CASAL sensitivity 1 model convergence information"
## [1] "Minimiser convergence threshold: 1e-006"                                                                  
## [2] "fmm: have converged: t = 4.30035e-007 f = 2296.34"                                                        
## [3] "Successful convergence in optimise"                                                                       
## [4] "Minimiser achieved convergence after 188 quasi-Newton iterations using 303 objective function evaluations"
## [1] ""
## [1] "Casal2 betadiff_casal_flags_on model convergence information"
## [1] "fmm: have converged: t = 0.00158129 f = 2296.97"
## [2] "Successful convergence in optimise"             
## [1] ""
## [1] "Casal2 betadiff_casal_flags_off model convergence information"
## [1] "fmm: have converged: t = 0.00158129 f = 2296.97"
## [2] "Successful convergence in optimise"             
## [1] ""
## [1] "Casal2 betadiff_casal_flags_on_low_tol model convergence information"
## [1] "fmm: have converged: t = 4.70876e-07 f = 2296.14"
## [2] "Successful convergence in optimise"              
## [1] ""
## [1] "Casal2 adolc_casal_flags_on model convergence information"
## character(0)
## [1] ""
## [1] "Casal2 adolc_casal_flags_off model convergence information"
## character(0)
## [1] ""
## [1] "Casal2 adolc_casal_flags_on_low_tol model convergence information"
## character(0)
## [1] "CASAL model warnings"
## NULL
## [1] ""
## [1] "CASAL sensitivity 1 model warnings"
##                        parameter estimate lower.bound upper.bound
## 1 selectivity[trawl_sel].male[3]      200           1         200
## [1] ""
## [1] "Casal2 betadiff_casal_flags_on model warnings"
## [1] ""
## [1] ""
## [1] "Casal2 betadiff_casal_flags_off model warnings"
## [1] ""
## [1] ""
## [1] "Casal2 betadiff_casal_flags_on_low_tol model warnings"
## [1] "estimated parameter 'selectivity[trwlFSel_m].sigma_r' was within 0.001 of upper bound 200"
## [2] "estimated parameter 'selectivity[trwlFSel_m].sigma_r' was within 0.001 of upper bound 200"
## [1] ""
## [1] "Casal2 adolc_casal_flags_on model warnings"
## [1] ""
## [1] ""
## [1] "Casal2 adolc_casal_flags_off model warnings"
## [1] ""
## [1] ""
## [1] "Casal2 adolc_casal_flags_on_low_tol model warnings"
## [1] "estimated parameter 'selectivity[trwlFSel_m].sigma_r' was within 0.001 of upper bound 200"
## [2] "estimated parameter 'selectivity[trwlFSel_m].sigma_r' was within 0.001 of upper bound 200"

1.5 Matching of outputs

Time series comparisons with CASAL base model results

## [1] "Catch time series base model comparison for run betadiff_casal_flags_on"
## [1] "Actual catches for trawl match: yes"
## [1] "Actual catches for line_home match: yes"
## [1] "Actual catches for line_spawn match: yes"
## [1] ""
## [1] "Catch time series base model comparison for run betadiff_casal_flags_off"
## [1] "Actual catches for trawl match: yes"
## [1] "Actual catches for line_home match: yes"
## [1] "Actual catches for line_spawn match: yes"
## [1] ""
## [1] "Catch time series base model comparison for run betadiff_casal_flags_on_low_tol"
## [1] "Actual catches for trawl match: yes"
## [1] "Actual catches for line_home match: yes"
## [1] "Actual catches for line_spawn match: yes"
## [1] ""
## [1] "Catch time series base model comparison for run adolc_casal_flags_on"
## [1] "Actual catches for trawl match: yes"
## [1] "Actual catches for line_home match: yes"
## [1] "Actual catches for line_spawn match: yes"
## [1] ""
## [1] "Catch time series base model comparison for run adolc_casal_flags_off"
## [1] "Actual catches for trawl match: yes"
## [1] "Actual catches for line_home match: yes"
## [1] "Actual catches for line_spawn match: yes"
## [1] ""
## [1] "Catch time series base model comparison for run adolc_casal_flags_on_low_tol"
## [1] "Actual catches for trawl match: yes"
## [1] "Actual catches for line_home match: yes"
## [1] "Actual catches for line_spawn match: yes"
## [1] ""

Derived quantities

SB0, SBcurrent, MSY, F_MSY, others…

1.6 Plots

Comparison plots

## [1] "CASAL base parameter correlation range (excluding 1.0): -0.7359 0.9329"

## [1] "CASAL sensitivity 1 parameter correlation range (excluding 1.0): -0.9871 0.9823"

## [1] "Casal2 betadiff_casal_flags_on parameter correlation range (excluding 1.0): -0.762745 0.93218"

## [1] "Casal2 betadiff_casal_flags_off parameter correlation range (excluding 1.0): -0.762745 0.93218"

## [1] "Casal2 betadiff_casal_flags_on_low_tol parameter correlation range (excluding 1.0): -0.989428 0.979127"

## [1] "Casal2 adolc_casal_flags_on parameter correlation range (excluding 1.0): -0.762745 0.93218"

## [1] "Casal2 adolc_casal_flags_off parameter correlation range (excluding 1.0): -0.762745 0.93218"

## [1] "Casal2 adolc_casal_flags_on_low_tol parameter correlation range (excluding 1.0): -0.989428 0.979127"